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[REVIEW]: OSCILOS_brass: an acoustic solver for brass instruments #3732

Closed whedon closed 1 year ago

whedon commented 3 years ago

Submitting author: !--author-handle-->@AlexanderMacL<!--end-author-handle-- (Alexander MacLaren) Repository: https://github.com/MorgansLab/OSCILOS_brass/ Branch with paper.md (empty if default branch): Version: v1.0 Editor: !--editor-->@vissarion<!--end-editor-- Reviewers: @astanziola, @drewbitllama, @krystophny Archive: Pending

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Markdown: [![status](https://joss.theoj.org/papers/6b3f5b373f35401ced225474bb953221/status.svg)](https://joss.theoj.org/papers/6b3f5b373f35401ced225474bb953221)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@astanziola & @drewbitllama, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @vissarion know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @astanziola

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @drewbitllama

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @astanziola, @drewbitllama it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (292.4 files/s, 39595.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                          20            496            519           2042
Markdown                         3             11              0             46
-------------------------------------------------------------------------------
SUM:                            23            507            519           2088
-------------------------------------------------------------------------------

Statistical information for the repository '1b2e3495b1b8e3c7967ef43c' was
gathered on 2021/09/16.
No commited files with the specified extensions were found.
whedon commented 3 years ago

PDF failed to compile for issue #3732 with the following error: 

 Can't find any papers to compile :-(
vissarion commented 3 years ago

@whedon generate pdf from branch Paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch Paper. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

vissarion commented 3 years ago

@whedon check references

drewbitllama commented 3 years ago

Hi all,

Apologies as I'm new to this process. I expressed interest in reviewing a paper, but I can't find a link to a PDF and the github repo I accepted seems basically empty :/

Can someone just send me a PDF so I can review the paper?

Thanks! Drew

On Thu, Sep 16, 2021 at 7:44 AM Vissarion Fisikopoulos < @.***> wrote:

@whedon https://github.com/whedon check references

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3732#issuecomment-920966891, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABQOYNXLMIXNA5B7ZFBT4ODUCH7E7ANCNFSM5EE5PHMA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

astanziola commented 3 years ago

Hello @drewbitllama The pdf is availabe a couple of messages above, in the last message from @whedon

Here's a link to the pdf

drewbitllama commented 3 years ago

Thanks Antonio!

I greatly appreciate that, I'll review the paper today.

Cheers, Drew

On Wed, Sep 22, 2021 at 9:13 AM Antonio Stanziola @.***> wrote:

Hello @drewbitllama https://github.com/drewbitllama The pdf is availabe a couple of messages above, in the last message from @whedon https://github.com/whedon

Here's a link to the pdf https://github.com/openjournals/joss-papers/blob/joss.03732/joss.03732/10.21105.joss.03732.pdf

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3732#issuecomment-925078289, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABQOYNWKRHSPMWAV4RURTTLUDH6DDANCNFSM5EE5PHMA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

astanziola commented 3 years ago

You're welcome Drew! That's the first time I review a JOSS paper too, it took a while to get an idea of what to do :smile:

drewbitllama commented 3 years ago

I appreciate your trailblazing!! I don't review papers too much anymore and this review process is -definitely- outside of my typical workflow. Thanks again!

On Wed, Sep 22, 2021 at 9:31 AM Antonio Stanziola @.***> wrote:

You're welcome Drew! That's the first time I review a JOSS paper too, it took a while to get an idea of what to do 😄

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3732#issuecomment-925092460, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABQOYNV73U5YOK4YFKFYQJDUDIAHNANCNFSM5EE5PHMA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

kthyng commented 3 years ago

@drewbitllama In case some more information would help — you'll want to look at the github review issue (linked at the bottom of any email you get about this review that comes from github). You can use the checklist at the top of this page to drive your review, opening issues on the software repository itself and then checking off boxes as you go (be sure to link to this review in the issues you open so everything is connected). The paper is a part of what you review, but only a small part; most of the review will be running and testing the software itself. Let me or @vissarion know if you have any questions.

vissarion commented 3 years ago

Thanks @kthyng for answering here!

@drewbitllama In case this is missed in the above discussions, I personally found the links below very useful the first time I did a JOSS review.

https://joss.readthedocs.io/en/latest/review_criteria.html https://joss.readthedocs.io/en/latest/review_checklist.html

whedon commented 3 years ago

:wave: @drewbitllama, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @astanziola, please update us on how your review is going (this is an automated reminder).

astanziola commented 3 years ago

Review is in process. I'm starting to add Issue on the author's repository, waiting feedback from them

vissarion commented 2 years ago

@drewbitllama @astanziola could you please update us on the review process?

astanziola commented 2 years ago

Hi @vissarion . I started to raise issues on the author's repository, but didn't have any feedback yet.

vissarion commented 2 years ago

Hi @AlexanderMacL we kindly need your feedback here.

AlexanderMacL commented 2 years ago

Hi @vissarion and @astanziola

My apologies - I have just realised that the repository submitted with the paper wasn't my personal one, so I've not been seeing notifications. Thanks so much for your help with the review. It looks to me like there's only one issue from astanziola on the repository on MorgansLab (yes, good idea, I'll list fsolve as a dependency in the paper). The issue text implied there would be more issues though. @astanziola could you let me know if I'm missing something? Many thanks

astanziola commented 2 years ago

Hi @AlexanderMacL ! I didn't raise other issues as I wasn't sure if this was stale, but will do it asap.

vissarion commented 2 years ago

:wave: @drewbitllama, @astanziola please update us on how your review is going.

vissarion commented 2 years ago

Hi, it has been some time of inactivity, I do not want to put pressure, I just want to ask if there is still interest to proceed with this review.

@AlexanderMacL there is an issue unresolved in the repository.

@astanziola are you done with the review? As far as I remember we are waiting for some more issues regarding the text.

@drewbitllama could you please complete your review list if you are still interested to review this paper.

May thanks for your time all of you!

vissarion commented 2 years ago

@arfon this issue seems abandoned, what do you recommend?

arfon commented 2 years ago

@AlexanderMacL – my understanding is that @vissarion been waiting for a number of weeks on your input here, and has been in contact over email to try and get your attention.

At this point I would like a re-confirmation from you in the next couple of weeks (by 28th June) that you're still interested in pursuing this publication with JOSS. Thank you!

AlexanderMacL commented 2 years ago

Hi Arfon, Vissarion,

Many thanks for your email, and my sincere apologies for missing your previous.

I am very much still interested in publishing this work - as of February this year it was unclear to me as to whether the reviews were complete, following Vissarion's email.

It looks like several reviewers were loathe to review MATLAB code, so it was difficult to get traction on this.

What are your thoughts on a Python port? Or Octave?

Thanks again, All the best, Alexander

On Tue, 14 Jun 2022, 17:14 Arfon Smith, @.***> wrote:

@AlexanderMacL https://github.com/AlexanderMacL – my understanding is that @vissarion https://github.com/vissarion been waiting for a number of weeks on your input here, and has been in contact over email to try and get your attention.

At this point I would like a re-confirmation from you in the next couple of weeks (by 28th June) that you're still interested in pursuing this publication with JOSS. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3732#issuecomment-1155718993, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMG7PTJJDLP3RGOJDWY6GVDVPDY3BANCNFSM5EE5PHMA . You are receiving this because you were mentioned.Message ID: @.***>

vissarion commented 2 years ago

Hi @AlexanderMacL, great that you are still interesting in publishing this work!

Regarding reviewers let me first ping the current reviewers once again.

Regarding the Python port or Octave I do not have experience but if that solution can be used without having MATLAB installed I think it will help a lot to find more reviewers (and will also broaden the user base of your package).

vissarion commented 2 years ago

:wave: @drewbitllama, @astanziola are you still interesting in finishing your reviews for this package?

arfon commented 1 year ago

@vissarion – it definitely looks like we need to find new reviewers here. What do you suggest as next steps?

vissarion commented 1 year ago

I will search a bit more for new reviewers. @AlexanderMacL please let me know if you have any suggestions.

vissarion commented 1 year ago

Hi @krystophny @pharshalp you are both experts in acoustics and matlab (that turned out to be a rare combination !), would you like to help us reviewing this submission for JOSS?

krystophny commented 1 year ago

Hi @krystophny @pharshalp you are both experts in acoustics and matlab (that turned out to be a rare combination !), would you like to help us reviewing this submission for JOSS?

Sure! Could take until beginning of November though, depending on free time slots.

vissarion commented 1 year ago

Hi @krystophny @pharshalp you are both experts in acoustics and matlab (that turned out to be a rare combination !), would you like to help us reviewing this submission for JOSS?

Sure! Could take until beginning of November though, depending on free time slots.

thanks OK, thanks! I am adding you.

@editorialbot add @krystophny as reviewer

vissarion commented 1 year ago

@editorialbot add @krystophny as reviewer

editorialbot commented 1 year ago

@krystophny added to the reviewers list!

vissarion commented 1 year ago

Hi @augucarv, @torbenwendt, @GLizaso, @jmrplens you are experts in acoustics and MATLAB, would you like to help us reviewing this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

augucarv commented 1 year ago

Hi @augucarv, @torbenwendt, @GLizaso, @jmrplens you are experts in acoustics and MATLAB, would you like to help us reviewing this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Hi @vissarion, I'm really short on time and won't be able to review it, sorry. Best of luck.

vissarion commented 1 year ago

Hi @krystophny could you please update us on your review progress? You have to run the following command in order to create you checklist @editorialbot generate my checklist and then fill it out during your review.

krystophny commented 1 year ago

Hi @krystophny could you please update us on your review progress? You have to run the following command in order to create you checklist @editorialbot generate my checklist and then fill it out during your review.

Thanks for the reminder, I’m now finally on it.

krystophny commented 1 year ago

Review checklist for @krystophny

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

krystophny commented 1 year ago

I am sorry that I have to propose to reject the submission in the current state. I am not willing to invest more any more time into this as a reviewer. The reasons are the following.

1) There are only few git commits, and not a single one is from the main author. Furthermore, it derives from another package OSCILOS_long, and it is not clear what code is re-used. I can therefore not verify the authors' contributions. 2) The software is not used in any peer-reviewed paper and seems to be known by very few users judging from the GitHub page. 3) There is no automated testing whatsoever, as the software is GUI-based in MATLAB. 4) The paper is minimalistic, with no background or references to other papers.

arfon commented 1 year ago

:wave: @AlexanderMacL @krystophny @vissarion – apologies it has taken so long to respond to this thread. After extensive discussion amongst the editorial team, we've taken the decision to reject this submission. Normally we would expect to make a decision like this following two recommendations to reject (i.e., from both reviewers) but given the feedback from @krystophny and the severe challenges we've had finding additional reviewers here we're making the decision to reject at this stage.

@astanziola, @drewbitllama, @krystophny, @vissarion – thank you for all of your efforts here.

arfon commented 1 year ago

@editorialbot reject

editorialbot commented 1 year ago

Paper rejected.